affy<-read.table("../AFFY/final.ind",sep=" ")
ill<-read.table("../ILL/final.ind",sep=" ")
dim(affy)
dim(ill)
affy<-affy[,c(1,2)]
ill<-ill[,c(1,2)]
rownames(affy)<-as.character(affy[,1])
rownames(ill)<-as.character(ill[,1])
rownames(ill)[1:5]
data<-read.table("../AFFY/affy_8000_after_concordance",sep="\t")
data1<-read.table("../ILL/ILL_8000_after_concordance",sep="\t")
dim(data)
dim(data1)
rownames(data)<-as.character(data[,1])
rownames(data1)<-as.character(data1[,1])
rownames(data1)[1:5]
rownames(data)[1:5]
affy1<-affy[rownames(data),]
affy[1:5,]
ill1<-ill[rownames(data1),]
ill1[1:5,]
summary(ill1[,2])
summary(affy1[,2])
rownames(affy1)[1:5]
affy1<-affy1[which(affy1[,2]>0.90),]
dim(affy1)
ill1<-ill1[which(ill1[,2]>0.90),]
dim(ill1)
summary(affy1[,2])
rownames(ill1)[1:5]
summary(ill1[,2])
rownames(affy1)[1:5]
data2<-data[rownames(rownames(affy1)),]
dim(data2)
data2<-data[which(rownames(affy1)),]
data2<-data[rownames(affy1),]
dim(data2)
data2[1:5,]
summary(data2[,2])
data12<-data1[rownames(ill1),]
summary(data12[,2])
dim(data12)
pdf("Concordance_r2gt90.pdf")
affy<-paste("AFFY CONCORCANCE;Num of snps",nrow(data2),sep=';')
ill<-paste("ILL CONCORCANCE;Num of snps",nrow(data112),sep=';')
ill<-paste("ILL CONCORCANCE;Num of snps",nrow(data12),sep=';')
hist(data2[,2],breaks=seq(0,1,0.001),xlim=c(0,1),ylim=c(0,1200),xlab="CONCORDANCE COUNTS",ylab ="counts",main=affy)
hist(data12[,2],breaks=seq(0,1,0.001),xlim=c(0,1),ylim=c(0,1200),xlab="CONCORDANCE COUNTS",ylab ="counts",main=ill)
dev.off()
savehistory("Concordance_r2gt90.R")
